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comparison GEMBASSY-1.0.3/src/gaaui.c @ 2:8947fca5f715 draft default tip

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
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1:84a17b3fad1f 2:8947fca5f715
1 /******************************************************************************
2 ** @source gaaui
3 **
4 ** Calculates various indeces of amino acid usage
5 **
6 ** @author Copyright (C) 2012 Hidetoshi Itaya
7 ** @version 1.0.3
8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
9 ** @modified 2013/6/16 Revision 1
10 ** @modified 2015/2/7 Refactor
11 ** @@
12 **
13 ** This program is free software; you can redistribute it and/or
14 ** modify it under the terms of the GNU General Public License
15 ** as published by the Free Software Foundation; either version 2
16 ** of the License, or (at your option) any later version.
17 **
18 ** This program is distributed in the hope that it will be useful,
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ** GNU General Public License for more details.
22 **
23 ** You should have received a copy of the GNU General Public License
24 ** along with this program; if not, write to the Free Software
25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
26 ******************************************************************************/
27
28 #include "emboss.h"
29 #include "glibs.h"
30
31
32
33
34 /* @prog gaaui ****************************************************************
35 **
36 ** Calculates various indeces of amino acid usage
37 **
38 ******************************************************************************/
39
40 int main(int argc, char *argv[])
41 {
42 embInitPV("gaaui", argc, argv, "GEMBASSY", "1.0.3");
43
44 AjPSeqall seqall;
45 AjPSeq seq;
46 AjPStr inseq = NULL;
47
48 AjBool accid = ajFalse;
49 AjPStr restid = NULL;
50 AjPStr seqid = NULL;
51
52 AjPStr base = NULL;
53 AjPStr url = NULL;
54
55 AjPFile tmpfile = NULL;
56 AjPStr tmpname = NULL;
57
58 AjPFile outf = NULL;
59
60 seqall = ajAcdGetSeqall("sequence");
61 accid = ajAcdGetBoolean("accid");
62 outf = ajAcdGetOutfile("outfile");
63
64 base = ajStrNewC("rest.g-language.org");
65
66 gAssignUniqueName(&tmpname);
67
68 while(ajSeqallNext(seqall, &seq))
69 {
70 inseq = NULL;
71
72 if(!accid)
73 {
74 if(gFormatGenbank(seq, &inseq))
75 {
76 tmpfile = ajFileNewOutNameS(tmpname);
77 if(!tmpfile)
78 {
79 ajDie("Output file (%S) open error\n", tmpname);
80 }
81 ajFmtPrintF(tmpfile, "%S", inseq);
82 ajFileClose(&tmpfile);
83 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
84 gFilePostSS(url, tmpname, &restid);
85 ajStrDel(&url);
86 ajSysFileUnlinkS(tmpname);
87 }
88 else
89 {
90 ajWarn("Sequence does not have features\n"
91 "Proceeding with sequence accession ID\n");
92 accid = ajTrue;
93 }
94 }
95
96 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
97
98 if(ajStrGetLen(seqid) == 0)
99 {
100 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
101 }
102
103 if(ajStrGetLen(seqid) == 0)
104 {
105 ajWarn("No valid header information\n");
106 }
107
108 if(accid)
109 {
110 ajStrAssignS(&restid, seqid);
111 if(ajStrGetLen(seqid) == 0)
112 {
113 ajDie("Cannot proceed without header with -accid\n");
114 }
115
116 if(!gValID(seqid))
117 {
118 ajDie("Invalid accession ID:%S, exiting\n", seqid);
119 }
120 }
121
122 url = ajStrNew();
123
124 ajFmtPrintS(&url, "http://%S/%S/aaui/output=f/tag=gene", base, restid);
125
126 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
127 if(!gFileOutURLS(url, &outf))
128 {
129 ajDie("Failed to download result from:\n%S\n", url);
130 }
131
132 ajStrDel(&url);
133 ajStrDel(&restid);
134 ajStrDel(&seqid);
135 ajStrDel(&inseq);
136 }
137
138 ajFileClose(&outf);
139
140 ajSeqallDel(&seqall);
141 ajSeqDel(&seq);
142 ajStrDel(&base);
143
144 embExit();
145
146 return 0;
147 }